class CreateREF
{
    public:
        char * reference_file;                          //file name of the reference file
        int num_files_reference;                        //number of files in the reference set
        int num_gs;                                     //number of genus/species
        char * output_file_name;                        //name of library file
        short unsigned int k_min;
        short unsigned int k_max;
        char ** taxa;                                   //decryption table for code representation of genus/species
        bool use_default_LLmult;                        //true=use default multiplier for legoland. false=set own
        int read_size;                                  //size of reads to be considered for the genome

        short unsigned int gc_dim1;                     //GC content to create dimension 1
        short unsigned int gc_dim2;                     //GC content to create dimension 2
        char * gc_dim1_file;                            //GC content dimension 1 file name
        char * gc_dim2_file;                            //GC content dimension 2 file name

        CreateREF();
        ~CreateREF();

    private:
        bool load_taxa();
        bool get_reference_file();
        bool get_parameters();
        bool get_advanced_parameters();
        bool create_reference_library();
};
